Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.16, per 1000 atoms: 0.64 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 336.7 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 454 0.90 - 1.17: 1203 1.17 - 1.44: 682 1.44 - 1.70: 798 1.70 - 1.97: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.329 1.121 0.208 1.00e-02 1.00e+04 4.32e+02 bond pdb=" N PRO A 127 " pdb=" CD PRO A 127 " ideal model delta sigma weight residual 1.473 1.198 0.275 1.40e-02 5.10e+03 3.85e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.234 1.017 0.216 1.22e-02 6.72e+03 3.15e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.189 0.189 1.10e-02 8.26e+03 2.95e+02 bond pdb=" C BTYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 1.333 1.584 -0.251 1.49e-02 4.50e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 2960 4.24 - 8.48: 1845 8.48 - 12.72: 762 12.72 - 16.96: 180 16.96 - 21.20: 30 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.07 108.45 11.62 7.10e-01 1.98e+00 2.68e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 137.39 -14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 106.48 12.72 9.00e-01 1.23e+00 2.00e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 122.93 108.17 14.76 1.06e+00 8.90e-01 1.94e+02 angle pdb=" O LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " ideal model delta sigma weight residual 120.85 134.61 -13.76 1.01e+00 9.80e-01 1.86e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.66: 916 15.66 - 31.32: 128 31.32 - 46.97: 46 46.97 - 62.63: 19 62.63 - 78.28: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -155.46 -24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.244: 104 0.244 - 0.485: 83 0.485 - 0.725: 39 0.725 - 0.966: 15 0.966 - 1.206: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.38 -1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.57 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA ALA A 6 " pdb=" N ALA A 6 " pdb=" C ALA A 6 " pdb=" CB ALA A 6 " both_signs ideal model delta sigma weight residual False 2.48 3.44 -0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.049 2.00e-02 2.50e+03 7.54e-02 1.71e+02 pdb=" CG PHE A 119 " -0.127 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.071 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.053 2.00e-02 2.50e+03 6.15e-02 1.14e+02 pdb=" CG ATYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.132 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.056 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.031 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.072 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.055 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" CG TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.086 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.093 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.068 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.014 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 911 2.30 - 2.87: 7913 2.87 - 3.45: 10588 3.45 - 4.02: 15323 4.02 - 4.60: 21834 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.719 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.823 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.830 2.450 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.844 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.849 2.100 ... (remaining 56564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_9291273_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792439 | | target function (ml) not normalized (work): 232626.927135 | | target function (ml) not normalized (free): 11831.385904 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3036 0.2090 7.1262 4.9478| | 2: 3.57 - 2.84 1.00 2876 122 0.2440 0.1644 4.341 4.3228| | 3: 2.84 - 2.48 1.00 2833 165 0.2364 0.1863 4.1214 4.1635| | 4: 2.47 - 2.25 1.00 2825 136 0.2369 0.1438 3.826 3.8255| | 5: 2.25 - 2.09 1.00 2756 127 0.2525 0.1622 3.7917 3.8399| | 6: 2.09 - 1.97 1.00 2846 113 0.2540 0.1774 3.4715 3.5246| | 7: 1.97 - 1.87 1.00 2787 165 0.2520 0.1752 3.1403 3.1589| | 8: 1.87 - 1.79 1.00 2789 144 0.2438 0.1766 3.06 3.0925| | 9: 1.79 - 1.72 1.00 2745 138 0.2422 0.1735 2.8941 2.9325| | 10: 1.72 - 1.66 1.00 2789 158 0.2424 0.2040 2.8178 2.9543| | 11: 1.66 - 1.61 1.00 2740 147 0.2436 0.1800 2.7563 2.7458| | 12: 1.61 - 1.56 1.00 2787 146 0.2516 0.2139 2.6248 2.6839| | 13: 1.56 - 1.52 1.00 2745 130 0.2583 0.1976 2.5723 2.6184| | 14: 1.52 - 1.48 1.00 2803 134 0.2600 0.2028 2.4909 2.5498| | 15: 1.48 - 1.45 1.00 2738 128 0.2595 0.1951 2.4457 2.4232| | 16: 1.45 - 1.42 1.00 2756 161 0.2643 0.2026 2.3791 2.3895| | 17: 1.42 - 1.39 1.00 2785 139 0.2651 0.2153 2.3182 2.3851| | 18: 1.39 - 1.36 1.00 2741 179 0.2668 0.2399 2.2589 2.448| | 19: 1.36 - 1.34 1.00 2807 134 0.2678 0.2438 2.2447 2.3404| | 20: 1.34 - 1.32 1.00 2696 147 0.2709 0.2237 2.2062 2.1863| | 21: 1.32 - 1.30 1.00 2785 112 0.2709 0.2272 2.1597 2.1788| | 22: 1.29 - 1.27 1.00 2704 152 0.2787 0.2477 2.1338 2.212| | 23: 1.27 - 1.26 1.00 2802 156 0.2788 0.2537 2.1021 2.1933| | 24: 1.26 - 1.24 1.00 2744 132 0.2748 0.2344 2.0727 2.0888| | 25: 1.24 - 1.22 1.00 2734 148 0.2848 0.2553 2.0511 2.0724| | 26: 1.22 - 1.21 1.00 2727 135 0.2817 0.2231 2.0081 2.0755| | 27: 1.21 - 1.19 1.00 2814 148 0.2959 0.2636 2.0162 2.0139| | 28: 1.19 - 1.18 1.00 2671 147 0.2928 0.2865 1.9814 2.0253| | 29: 1.18 - 1.16 1.00 2800 134 0.3030 0.2847 1.9691 2.0339| | 30: 1.16 - 1.15 1.00 2740 148 0.3079 0.3095 1.9325 2.0017| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.61 0.76 0.23 1454.08| | 2: 3.57 - 2.84 2876 122 0.81 25.81 1.27 0.23 1454.08| | 3: 2.84 - 2.48 2833 165 0.74 31.73 1.24 0.24 1206.10| | 4: 2.47 - 2.25 2825 136 0.81 25.44 1.26 0.25 562.56| | 5: 2.25 - 2.09 2756 127 0.77 29.16 1.29 0.25 562.56| | 6: 2.09 - 1.97 2846 113 0.84 22.58 1.29 0.25 308.53| | 7: 1.97 - 1.87 2787 165 0.90 16.67 1.28 0.25 91.88| | 8: 1.87 - 1.79 2789 144 0.86 21.08 1.24 0.25 91.88| | 9: 1.79 - 1.72 2745 138 0.88 18.75 1.24 0.25 55.63| | 10: 1.72 - 1.66 2789 158 0.87 20.11 1.22 0.25 48.37| | 11: 1.66 - 1.61 2740 147 0.86 21.22 1.22 0.25 46.67| | 12: 1.61 - 1.56 2787 146 0.88 18.70 1.23 0.25 29.37| | 13: 1.56 - 1.52 2745 130 0.87 20.28 1.25 0.25 29.37| | 14: 1.52 - 1.48 2803 134 0.86 20.77 1.25 0.25 26.19| | 15: 1.48 - 1.45 2738 128 0.88 19.64 1.23 0.25 20.38| | 16: 1.45 - 1.42 2756 161 0.86 21.53 1.24 0.25 20.38| | 17: 1.42 - 1.39 2785 139 0.87 20.60 1.23 0.25 17.69| | 18: 1.39 - 1.36 2741 179 0.86 21.54 1.24 0.25 16.14| | 19: 1.36 - 1.34 2807 134 0.85 22.49 1.22 0.25 16.14| | 20: 1.34 - 1.32 2696 147 0.87 21.10 1.21 0.25 13.34| | 21: 1.32 - 1.30 2785 112 0.86 22.15 1.21 0.25 13.15| | 22: 1.29 - 1.27 2704 152 0.85 22.89 1.22 0.24 12.88| | 23: 1.27 - 1.26 2802 156 0.85 22.95 1.21 0.24 11.52| | 24: 1.26 - 1.24 2744 132 0.84 23.31 1.20 0.24 11.52| | 25: 1.24 - 1.22 2734 148 0.84 24.02 1.21 0.24 10.97| | 26: 1.22 - 1.21 2727 135 0.83 24.73 1.19 0.23 10.35| | 27: 1.21 - 1.19 2814 148 0.82 25.65 1.20 0.23 10.35| | 28: 1.19 - 1.18 2671 147 0.81 26.61 1.18 0.22 9.93| | 29: 1.18 - 1.16 2800 134 0.80 27.61 1.17 0.22 9.77| | 30: 1.16 - 1.15 2740 148 0.79 29.02 1.16 0.22 9.77| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.77 max = 1454.08 mean = 211.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.89| |phase err.(test): min = 0.00 max = 89.19 mean = 22.71| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.275 1557 Z= 5.463 Angle : 5.274 19.994 2118 Z= 3.722 Chirality : 0.402 1.206 243 Planarity : 0.031 0.090 284 Dihedral : 13.567 78.285 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.45), residues: 224 helix: -2.85 (0.34), residues: 108 sheet: -2.04 (0.68), residues: 30 loop : -0.39 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.019 ARG A 5 TYR 0.076 0.045 TYR A 141 PHE 0.119 0.031 PHE A 119 HIS 0.069 0.020 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792439 | | target function (ml) not normalized (work): 232626.927135 | | target function (ml) not normalized (free): 11831.385904 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2613 0.1947 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2613 0.1947 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1947 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2007 0.2011 0.1960 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1638 0.1779 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1638 0.1779 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3831 386.444 357.272 0.679 1.003 0.420 11.894-9.307 99.02 97 4 0.1817 613.847 589.971 0.925 1.003 0.388 9.237-7.194 100.00 213 7 0.2215 502.052 490.702 0.960 1.004 0.369 7.162-5.571 100.00 427 22 0.2169 376.762 366.367 0.925 1.004 0.288 5.546-4.326 100.00 867 58 0.1252 517.201 512.224 0.963 1.004 0.238 4.315-3.360 100.00 1859 96 0.1144 491.862 488.463 1.005 1.003 0.222 3.356-2.611 100.00 3867 181 0.1459 323.128 319.658 0.996 1.002 0.052 2.608-2.026 99.99 8198 413 0.1349 214.204 212.039 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1652 104.606 103.949 1.009 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2062 46.387 45.084 1.007 0.995 0.000 1.221-1.150 99.97 13689 708 0.2583 29.227 26.926 0.974 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0450 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1638 r_free=0.1779 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1640 r_free=0.1786 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.174195 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1999.648476 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1458 0.0247 0.007 1.0 1.0 0.5 0.0 0 12.587 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.58 2.47 3.013 19.055 1999.648 0.017 12.45 15.34 2.89 3.392 19.654 1999.648 0.016 Individual atomic B min max mean iso aniso Overall: 8.58 118.49 21.22 2.91 0 1785 Protein: 8.58 118.49 18.05 2.91 0 1519 Water: 11.15 114.50 39.57 N/A 0 258 Other: 23.35 37.99 30.18 N/A 0 8 Chain A: 8.58 118.49 21.22 N/A 0 1785 Histogram: Values Number of atoms 8.58 - 19.57 1204 19.57 - 30.56 232 30.56 - 41.56 153 41.56 - 52.55 108 52.55 - 63.54 53 63.54 - 74.53 19 74.53 - 85.52 9 85.52 - 96.51 2 96.51 - 107.50 2 107.50 - 118.49 3 =========================== Idealize ADP of riding H ========================== r_work=0.1246 r_free=0.1534 r_work=0.1250 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1250 r_free = 0.1539 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1248 r_free = 0.1542 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1248 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015427 | | target function (ls_wunit_k1) not normalized (work): 1285.045313 | | target function (ls_wunit_k1) not normalized (free): 114.068195 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1248 0.1542 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1712 0.1711 0.1774 n_refl.: 87593 remove outliers: r(all,work,free)=0.1712 0.1711 0.1774 n_refl.: 87593 overall B=0.11 to atoms: r(all,work,free)=0.1731 0.1730 0.1787 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1246 0.1532 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1245 0.1532 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3573 298.052 278.563 0.634 1.002 0.380 11.894-9.307 99.02 97 4 0.1614 477.463 466.599 0.905 1.002 0.369 9.237-7.194 100.00 213 7 0.1828 390.506 385.145 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1689 293.053 288.228 0.924 1.003 0.254 5.546-4.326 100.00 867 58 0.0905 402.289 399.840 0.949 1.003 0.214 4.315-3.360 100.00 1859 96 0.0770 382.580 381.611 0.996 1.002 0.200 3.356-2.611 100.00 3867 181 0.1023 251.335 250.598 0.998 1.002 0.100 2.608-2.026 99.99 8198 413 0.0981 166.612 165.985 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1217 81.365 81.527 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1655 36.080 35.537 1.007 0.999 0.000 1.221-1.150 99.97 13689 708 0.2363 22.733 21.243 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0439 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1532 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1245 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1532 | n_water=258 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1254 r_free=0.1530 | n_water=252 | time (s): 26.170 (total time: 28.590) Filter (q & B) r_work=0.1257 r_free=0.1529 | n_water=249 | time (s): 3.690 (total time: 32.280) Compute maps r_work=0.1257 r_free=0.1529 | n_water=249 | time (s): 1.810 (total time: 34.090) Filter (map) r_work=0.1279 r_free=0.1546 | n_water=235 | time (s): 3.770 (total time: 37.860) Find peaks r_work=0.1279 r_free=0.1546 | n_water=235 | time (s): 0.710 (total time: 38.570) Add new water r_work=0.1436 r_free=0.1704 | n_water=460 | time (s): 3.540 (total time: 42.110) Refine new water occ: r_work=0.1335 r_free=0.1540 adp: r_work=0.1253 r_free=0.1502 occ: r_work=0.1266 r_free=0.1495 adp: r_work=0.1230 r_free=0.1481 occ: r_work=0.1233 r_free=0.1472 adp: r_work=0.1223 r_free=0.1470 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1470 r_work=0.1223 r_free=0.1470 | n_water=460 | time (s): 91.260 (total time: 133.370) Filter (q & B) r_work=0.1230 r_free=0.1483 | n_water=436 | time (s): 3.880 (total time: 137.250) Filter (dist only) r_work=0.1230 r_free=0.1483 | n_water=436 | time (s): 40.720 (total time: 177.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.298018 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1502.506274 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1511 0.0281 0.007 0.9 1.9 0.5 0.0 0 12.649 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.11 2.81 3.833 23.406 1502.506 0.015 12.04 14.89 2.85 4.294 23.186 1502.506 0.015 Individual atomic B min max mean iso aniso Overall: 8.69 113.61 23.38 2.60 201 1762 Protein: 8.69 113.61 17.77 2.61 0 1519 Water: 11.25 71.70 42.85 N/A 201 235 Other: 23.73 34.93 28.47 N/A 0 8 Chain A: 8.69 113.61 20.52 N/A 0 1762 Chain S: 20.10 71.70 48.46 N/A 201 0 Histogram: Values Number of atoms 8.69 - 19.18 1201 19.18 - 29.67 251 29.67 - 40.16 179 40.16 - 50.66 147 50.66 - 61.15 116 61.15 - 71.64 56 71.64 - 82.13 6 82.13 - 92.62 3 92.62 - 103.11 2 103.11 - 113.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1490 r_work=0.1205 r_free=0.1489 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1489 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1483 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1208 r_free= 0.1483 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014031 | | target function (ls_wunit_k1) not normalized (work): 1168.740064 | | target function (ls_wunit_k1) not normalized (free): 102.619871 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1208 0.1483 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1620 0.1616 0.1730 n_refl.: 87592 remove outliers: r(all,work,free)=0.1620 0.1616 0.1730 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1625 0.1621 0.1733 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1204 0.1481 n_refl.: 87592 remove outliers: r(all,work,free)=0.1216 0.1203 0.1481 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3318 290.771 272.530 0.628 0.937 0.358 11.894-9.307 99.02 97 4 0.1505 477.463 473.877 0.986 0.938 0.357 9.237-7.194 100.00 213 7 0.1686 390.506 390.924 1.040 0.938 0.290 7.162-5.571 100.00 427 22 0.1456 293.053 289.190 1.006 0.938 0.235 5.546-4.326 100.00 867 58 0.0833 402.289 399.364 1.022 0.938 0.220 4.315-3.360 100.00 1859 96 0.0725 382.580 381.426 1.068 0.939 0.210 3.356-2.611 100.00 3867 181 0.0961 251.335 250.617 1.075 0.940 0.150 2.608-2.026 99.99 8198 413 0.0971 166.612 166.180 1.084 0.941 0.000 2.025-1.573 100.00 17313 902 0.1187 81.365 81.545 1.089 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1617 36.080 35.580 1.073 0.946 0.000 1.221-1.150 99.97 13689 708 0.2344 22.733 21.289 1.028 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0526 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1481 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1481 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1481 | n_water=436 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1204 r_free=0.1479 | n_water=434 | time (s): 40.190 (total time: 41.880) Filter (q & B) r_work=0.1205 r_free=0.1480 | n_water=433 | time (s): 3.040 (total time: 44.920) Compute maps r_work=0.1205 r_free=0.1480 | n_water=433 | time (s): 1.430 (total time: 46.350) Filter (map) r_work=0.1241 r_free=0.1486 | n_water=295 | time (s): 3.450 (total time: 49.800) Find peaks r_work=0.1241 r_free=0.1486 | n_water=295 | time (s): 0.660 (total time: 50.460) Add new water r_work=0.1370 r_free=0.1593 | n_water=483 | time (s): 3.560 (total time: 54.020) Refine new water occ: r_work=0.1268 r_free=0.1503 adp: r_work=0.1269 r_free=0.1505 occ: r_work=0.1245 r_free=0.1482 adp: r_work=0.1243 r_free=0.1483 occ: r_work=0.1229 r_free=0.1471 adp: r_work=0.1222 r_free=0.1467 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1467 r_work=0.1222 r_free=0.1467 | n_water=483 | time (s): 194.020 (total time: 248.040) Filter (q & B) r_work=0.1226 r_free=0.1469 | n_water=454 | time (s): 2.990 (total time: 251.030) Filter (dist only) r_work=0.1226 r_free=0.1468 | n_water=453 | time (s): 39.060 (total time: 290.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.956576 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.806778 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1430 0.0198 0.006 0.9 2.2 0.5 0.0 0 0.978 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.30 1.98 3.638 22.286 46.807 3.722 12.22 13.94 1.72 4.245 22.064 46.807 3.653 Individual atomic B min max mean iso aniso Overall: 9.27 108.64 21.85 2.33 221 1759 Protein: 9.27 108.64 17.25 2.33 0 1519 Water: 11.51 69.85 37.21 N/A 221 232 Other: 19.94 31.37 25.69 N/A 0 8 Chain A: 9.27 108.64 19.95 N/A 0 1759 Chain S: 15.92 65.61 36.98 N/A 221 0 Histogram: Values Number of atoms 9.27 - 19.20 1229 19.20 - 29.14 273 29.14 - 39.08 216 39.08 - 49.02 141 49.02 - 58.95 84 58.95 - 68.89 24 68.89 - 78.83 7 78.83 - 88.76 2 88.76 - 98.70 2 98.70 - 108.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1222 r_free=0.1394 r_work=0.1223 r_free=0.1395 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1223 r_free = 0.1395 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1216 r_free = 0.1392 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1216 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.649315 | | target function (ml) not normalized (work): 303958.776678 | | target function (ml) not normalized (free): 16053.109246 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1216 0.1392 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1553 0.1551 0.1613 n_refl.: 87588 remove outliers: r(all,work,free)=0.1553 0.1551 0.1613 n_refl.: 87588 overall B=-0.02 to atoms: r(all,work,free)=0.1550 0.1548 0.1611 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1209 0.1373 n_refl.: 87588 remove outliers: r(all,work,free)=0.1214 0.1206 0.1373 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3634 285.299 255.615 0.472 1.000 0.305 11.894-9.307 97.06 95 4 0.2382 477.684 455.546 0.856 1.001 0.287 9.237-7.194 98.64 210 7 0.2346 383.071 384.224 0.950 1.002 0.190 7.162-5.571 100.00 427 22 0.1958 293.053 284.392 0.918 1.002 0.181 5.546-4.326 100.00 867 58 0.1079 402.289 398.251 0.954 1.002 0.180 4.315-3.360 100.00 1859 96 0.0936 382.580 379.946 0.992 1.002 0.180 3.356-2.611 100.00 3867 181 0.1174 251.335 249.466 0.999 1.002 0.072 2.608-2.026 99.99 8198 413 0.1068 166.612 165.591 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1027 81.365 81.512 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1298 36.080 35.653 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2132 22.733 21.343 0.981 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0403 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1206 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1373 | n_water=453 | time (s): 1.970 (total time: 1.970) Filter (dist) r_work=0.1206 r_free=0.1373 | n_water=452 | time (s): 37.260 (total time: 39.230) Filter (q & B) r_work=0.1206 r_free=0.1373 | n_water=452 | time (s): 1.300 (total time: 40.530) Compute maps r_work=0.1206 r_free=0.1373 | n_water=452 | time (s): 1.620 (total time: 42.150) Filter (map) r_work=0.1223 r_free=0.1379 | n_water=327 | time (s): 2.640 (total time: 44.790) Find peaks r_work=0.1223 r_free=0.1379 | n_water=327 | time (s): 0.540 (total time: 45.330) Add new water r_work=0.1295 r_free=0.1425 | n_water=493 | time (s): 3.090 (total time: 48.420) Refine new water occ: r_work=0.1220 r_free=0.1362 adp: r_work=0.1220 r_free=0.1362 occ: r_work=0.1203 r_free=0.1353 adp: r_work=0.1202 r_free=0.1349 occ: r_work=0.1192 r_free=0.1353 adp: r_work=0.1188 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1346 r_work=0.1188 r_free=0.1346 | n_water=493 | time (s): 175.480 (total time: 223.900) Filter (q & B) r_work=0.1195 r_free=0.1350 | n_water=460 | time (s): 3.240 (total time: 227.140) Filter (dist only) r_work=0.1195 r_free=0.1349 | n_water=459 | time (s): 39.160 (total time: 266.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.900419 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.616966 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1364 0.0166 0.006 0.9 1.9 0.5 0.0 0 0.950 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.64 1.66 3.427 21.603 45.617 3.637 11.82 13.60 1.78 3.727 21.519 45.617 3.622 Individual atomic B min max mean iso aniso Overall: 9.30 104.30 21.50 2.17 228 1758 Protein: 9.30 104.30 17.03 2.18 0 1519 Water: 11.43 68.73 36.21 N/A 228 231 Other: 20.22 28.70 24.56 N/A 0 8 Chain A: 9.30 104.30 19.68 N/A 0 1758 Chain S: 15.24 58.05 35.53 N/A 228 0 Histogram: Values Number of atoms 9.30 - 18.80 1218 18.80 - 28.30 286 28.30 - 37.80 215 37.80 - 47.30 154 47.30 - 56.80 70 56.80 - 66.30 29 66.30 - 75.80 9 75.80 - 85.30 2 85.30 - 94.80 1 94.80 - 104.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1360 r_work=0.1182 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1360 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1176 r_free = 0.1358 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1176 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619900 | | target function (ml) not normalized (work): 301476.156915 | | target function (ml) not normalized (free): 15934.795174 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1185 0.1176 0.1358 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1497 0.1493 0.1593 n_refl.: 87579 remove outliers: r(all,work,free)=0.1497 0.1493 0.1593 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1494 0.1490 0.1591 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1175 0.1360 n_refl.: 87579 remove outliers: r(all,work,free)=0.1182 0.1173 0.1360 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3832 285.299 254.334 0.448 0.999 0.304 11.894-9.307 93.14 91 4 0.2233 477.987 454.189 0.850 1.001 0.232 9.237-7.194 98.18 209 7 0.2392 382.075 379.177 0.924 1.001 0.170 7.162-5.571 100.00 427 22 0.2083 293.053 283.546 0.912 1.002 0.140 5.546-4.326 100.00 867 58 0.1098 402.289 398.209 0.953 1.002 0.135 4.315-3.360 100.00 1859 96 0.0926 382.580 380.349 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1143 251.335 249.686 1.000 1.001 0.053 2.608-2.026 99.99 8198 413 0.1026 166.612 165.703 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0975 81.365 81.609 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.080 35.699 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2124 22.733 21.356 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0395 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1173 r_free=0.1360 After: r_work=0.1174 r_free=0.1360 ================================== NQH flips ================================== r_work=0.1174 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1174 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1174 r_free=0.1360 | n_water=459 | time (s): 1.740 (total time: 1.740) Filter (dist) r_work=0.1174 r_free=0.1360 | n_water=458 | time (s): 39.400 (total time: 41.140) Filter (q & B) r_work=0.1174 r_free=0.1360 | n_water=458 | time (s): 1.210 (total time: 42.350) Compute maps r_work=0.1174 r_free=0.1360 | n_water=458 | time (s): 1.260 (total time: 43.610) Filter (map) r_work=0.1200 r_free=0.1376 | n_water=341 | time (s): 3.550 (total time: 47.160) Find peaks r_work=0.1200 r_free=0.1376 | n_water=341 | time (s): 0.570 (total time: 47.730) Add new water r_work=0.1251 r_free=0.1421 | n_water=501 | time (s): 3.210 (total time: 50.940) Refine new water occ: r_work=0.1188 r_free=0.1357 adp: r_work=0.1188 r_free=0.1358 occ: r_work=0.1176 r_free=0.1348 adp: r_work=0.1175 r_free=0.1347 occ: r_work=0.1168 r_free=0.1342 adp: r_work=0.1164 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1340 r_work=0.1164 r_free=0.1340 | n_water=501 | time (s): 150.800 (total time: 201.740) Filter (q & B) r_work=0.1173 r_free=0.1342 | n_water=462 | time (s): 3.290 (total time: 205.030) Filter (dist only) r_work=0.1173 r_free=0.1341 | n_water=461 | time (s): 39.860 (total time: 244.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.956799 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.007867 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1362 0.0158 0.007 1.1 5.1 0.5 0.0 0 0.978 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.62 1.58 3.313 21.341 45.008 3.628 12.06 13.64 1.59 3.632 21.249 45.008 3.622 Individual atomic B min max mean iso aniso Overall: 9.30 100.16 21.26 2.03 230 1758 Protein: 9.30 100.16 16.76 2.03 0 1519 Water: 11.47 67.53 36.02 N/A 230 231 Other: 19.93 27.78 24.00 N/A 0 8 Chain A: 9.30 100.16 19.40 N/A 0 1758 Chain S: 14.20 58.92 35.49 N/A 230 0 Histogram: Values Number of atoms 9.30 - 18.38 1210 18.38 - 27.47 279 27.47 - 36.56 216 36.56 - 45.64 156 45.64 - 54.73 75 54.73 - 63.82 33 63.82 - 72.90 14 72.90 - 81.99 2 81.99 - 91.08 1 91.08 - 100.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1364 r_work=0.1206 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1364 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1363 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1203 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621154 | | target function (ml) not normalized (work): 301562.460891 | | target function (ml) not normalized (free): 15938.240436 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1408 0.1370 5.6766 5.6007| | 2: 3.57 - 2.84 1.00 2888 124 0.1120 0.1403 5.1862 5.2526| | 3: 2.83 - 2.48 1.00 2820 163 0.1254 0.1289 4.9975 5.0228| | 4: 2.47 - 2.25 1.00 2825 136 0.1041 0.1207 4.6997 4.7663| | 5: 2.25 - 2.09 1.00 2756 127 0.1012 0.1087 4.6375 4.6989| | 6: 2.09 - 1.97 1.00 2846 113 0.0983 0.1190 4.3473 4.455| | 7: 1.97 - 1.87 1.00 2787 165 0.0999 0.1229 4.0772 4.1815| | 8: 1.87 - 1.79 1.00 2789 144 0.1039 0.1288 3.9958 4.0929| | 9: 1.79 - 1.72 1.00 2745 138 0.0959 0.1267 3.7167 3.8941| | 10: 1.72 - 1.66 1.00 2831 160 0.1013 0.1230 3.639 3.7575| | 11: 1.66 - 1.61 1.00 2712 147 0.0968 0.1129 3.5741 3.6253| | 12: 1.61 - 1.56 1.00 2773 144 0.0917 0.1177 3.352 3.4857| | 13: 1.56 - 1.52 1.00 2745 130 0.0989 0.1111 3.3435 3.4623| | 14: 1.52 - 1.48 1.00 2803 134 0.0995 0.1128 3.2655 3.3471| | 15: 1.48 - 1.45 1.00 2738 128 0.1024 0.1342 3.1762 3.3168| | 16: 1.45 - 1.42 1.00 2756 161 0.1075 0.1298 3.159 3.2658| | 17: 1.42 - 1.39 1.00 2785 139 0.1127 0.1307 3.1197 3.2385| | 18: 1.39 - 1.36 1.00 2741 179 0.1162 0.1383 3.0875 3.2642| | 19: 1.36 - 1.34 1.00 2807 134 0.1223 0.1573 3.0955 3.2597| | 20: 1.34 - 1.32 1.00 2696 147 0.1320 0.1441 3.0879 3.1296| | 21: 1.32 - 1.30 1.00 2785 112 0.1421 0.1654 3.089 3.1646| | 22: 1.29 - 1.27 1.00 2704 152 0.1483 0.1944 3.0856 3.2935| | 23: 1.27 - 1.26 1.00 2802 156 0.1574 0.1879 3.1016 3.2101| | 24: 1.26 - 1.24 1.00 2744 132 0.1623 0.1770 3.0921 3.2039| | 25: 1.24 - 1.22 1.00 2733 148 0.1792 0.2296 3.1065 3.2888| | 26: 1.22 - 1.21 1.00 2727 135 0.1856 0.1802 3.1197 3.2009| | 27: 1.21 - 1.19 1.00 2814 148 0.2018 0.2108 3.1401 3.1539| | 28: 1.19 - 1.18 1.00 2671 147 0.2151 0.2316 3.1397 3.1657| | 29: 1.18 - 1.16 1.00 2800 134 0.2218 0.2371 3.1233 3.2212| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2476 3.1117 3.1602| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2916 171 0.95 8.72 1.00 0.97 5934.73| | 2: 3.57 - 2.84 2888 124 0.92 12.95 1.01 0.97 5934.73| | 3: 2.83 - 2.48 2820 163 0.89 17.14 0.99 0.97 4983.92| | 4: 2.47 - 2.25 2825 136 0.91 14.33 1.00 0.97 2532.09| | 5: 2.25 - 2.09 2756 127 0.90 16.52 1.01 0.97 2532.09| | 6: 2.09 - 1.97 2846 113 0.92 13.54 1.02 0.97 1504.03| | 7: 1.97 - 1.87 2787 165 0.94 10.87 1.02 0.97 627.24| | 8: 1.87 - 1.79 2789 144 0.91 14.48 1.00 0.97 627.24| | 9: 1.79 - 1.72 2745 138 0.93 11.50 0.98 0.97 341.86| | 10: 1.72 - 1.66 2831 160 0.93 12.36 0.98 0.97 284.71| | 11: 1.66 - 1.61 2712 147 0.93 12.98 0.98 0.97 271.84| | 12: 1.61 - 1.56 2773 144 0.95 9.71 0.99 0.97 150.38| | 13: 1.56 - 1.52 2745 130 0.94 11.30 1.02 0.97 150.38| | 14: 1.52 - 1.48 2803 134 0.94 11.50 1.02 0.97 134.44| | 15: 1.48 - 1.45 2738 128 0.95 10.63 1.02 0.98 105.26| | 16: 1.45 - 1.42 2756 161 0.94 11.85 1.02 0.98 105.26| | 17: 1.42 - 1.39 2785 139 0.94 11.65 1.01 0.98 94.73| | 18: 1.39 - 1.36 2741 179 0.94 11.95 1.01 0.98 88.64| | 19: 1.36 - 1.34 2807 134 0.94 12.50 1.00 0.98 88.64| | 20: 1.34 - 1.32 2696 147 0.94 12.56 0.99 0.96 83.12| | 21: 1.32 - 1.30 2785 112 0.93 13.48 0.98 0.96 82.73| | 22: 1.29 - 1.27 2704 152 0.93 14.07 0.98 0.96 82.86| | 23: 1.27 - 1.26 2802 156 0.92 14.93 0.98 0.94 83.55| | 24: 1.26 - 1.24 2744 132 0.92 15.09 0.97 0.94 83.55| | 25: 1.24 - 1.22 2733 148 0.91 16.51 0.96 0.94 85.01| | 26: 1.22 - 1.21 2727 135 0.90 18.19 1.02 0.93 86.63| | 27: 1.21 - 1.19 2814 148 0.89 18.88 1.02 0.93 86.63| | 28: 1.19 - 1.18 2671 147 0.88 20.37 1.01 0.93 89.68| | 29: 1.18 - 1.16 2800 134 0.88 20.67 0.99 0.92 90.83| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.92 90.83| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.73 max = 5934.73 mean = 936.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 14.09| |phase err.(test): min = 0.00 max = 89.68 mean = 14.23| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1203 0.1363 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1511 0.1508 0.1582 n_refl.: 87574 remove outliers: r(all,work,free)=0.1511 0.1508 0.1582 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1509 0.1506 0.1580 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1204 0.1364 n_refl.: 87574 remove outliers: r(all,work,free)=0.1212 0.1204 0.1364 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3928 285.299 256.721 0.436 0.998 0.281 11.894-9.307 92.16 90 4 0.2455 474.236 459.734 0.856 1.000 0.186 9.237-7.194 98.18 209 7 0.2513 382.075 375.838 0.914 1.000 0.120 7.162-5.571 100.00 427 22 0.2197 293.053 282.228 0.900 1.001 0.120 5.546-4.326 100.00 867 58 0.1186 402.289 397.507 0.953 1.001 0.120 4.315-3.360 100.00 1859 96 0.0994 382.580 379.841 0.995 1.001 0.120 3.356-2.611 100.00 3867 181 0.1199 251.335 249.254 1.000 1.001 0.043 2.608-2.026 99.99 8198 413 0.1056 166.612 165.584 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0987 81.365 81.591 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.080 35.711 1.020 1.000 0.000 1.221-1.150 99.97 13689 708 0.2122 22.733 21.320 0.974 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0363 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2612 0.1947 0.083 5.274 8.8 119.3 19.9 258 0.000 1_bss: 0.1638 0.1779 0.083 5.274 9.0 119.5 20.1 258 0.000 1_settarget: 0.1638 0.1779 0.083 5.274 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1786 0.083 5.274 9.0 119.5 20.1 258 0.003 1_weight: 0.1640 0.1786 0.083 5.274 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1212 0.1458 0.007 0.963 9.0 119.5 20.1 258 0.125 1_adp: 0.1246 0.1534 0.007 0.963 8.6 118.5 21.2 258 0.125 1_regHadp: 0.1250 0.1539 0.007 0.963 8.6 118.5 21.2 258 0.125 1_occ: 0.1248 0.1542 0.007 0.963 8.6 118.5 21.2 258 0.125 2_bss: 0.1245 0.1532 0.007 0.963 8.7 118.6 21.3 258 0.125 2_settarget: 0.1245 0.1532 0.007 0.963 8.7 118.6 21.3 258 0.125 2_updatecdl: 0.1245 0.1532 0.007 0.954 8.7 118.6 21.3 258 0.125 2_nqh: 0.1245 0.1532 0.007 0.954 8.7 118.6 21.3 258 0.125 2_sol: 0.1230 0.1483 0.007 0.954 8.7 118.6 23.8 436 n/a 2_weight: 0.1230 0.1483 0.007 0.954 8.7 118.6 23.8 436 n/a 2_xyzrec: 0.1230 0.1511 0.007 0.875 8.7 118.6 23.8 436 n/a 2_adp: 0.1205 0.1490 0.007 0.875 8.7 113.6 23.4 436 n/a 2_regHadp: 0.1205 0.1489 0.007 0.875 8.7 113.6 23.4 436 n/a 2_occ: 0.1208 0.1483 0.007 0.875 8.7 113.6 23.4 436 n/a 3_bss: 0.1203 0.1481 0.007 0.875 8.7 113.6 23.4 436 n/a 3_settarget: 0.1203 0.1481 0.007 0.875 8.7 113.6 23.4 436 n/a 3_updatecdl: 0.1203 0.1481 0.007 0.876 8.7 113.6 23.4 436 n/a 3_nqh: 0.1203 0.1481 0.007 0.876 8.7 113.6 23.4 436 n/a 3_sol: 0.1226 0.1468 0.007 0.876 8.7 113.6 22.2 453 n/a 3_weight: 0.1226 0.1468 0.007 0.876 8.7 113.6 22.2 453 n/a 3_xyzrec: 0.1232 0.1430 0.006 0.910 8.7 113.6 22.2 453 n/a 3_adp: 0.1222 0.1394 0.006 0.910 9.3 108.6 21.8 453 n/a 3_regHadp: 0.1223 0.1395 0.006 0.910 9.3 108.6 21.8 453 n/a 3_occ: 0.1216 0.1392 0.006 0.910 9.3 108.6 21.8 453 n/a 4_bss: 0.1206 0.1373 0.006 0.910 9.3 108.6 21.8 453 n/a 4_settarget: 0.1206 0.1373 0.006 0.910 9.3 108.6 21.8 453 n/a 4_updatecdl: 0.1206 0.1373 0.006 0.908 9.3 108.6 21.8 453 n/a 4_nqh: 0.1206 0.1373 0.006 0.908 9.3 108.6 21.8 453 n/a 4_sol: 0.1195 0.1349 0.006 0.908 9.3 108.6 21.6 459 n/a 4_weight: 0.1195 0.1349 0.006 0.908 9.3 108.6 21.6 459 n/a 4_xyzrec: 0.1198 0.1364 0.006 0.949 9.3 108.6 21.6 459 n/a 4_adp: 0.1182 0.1360 0.006 0.949 9.3 104.3 21.5 459 n/a 4_regHadp: 0.1182 0.1360 0.006 0.949 9.3 104.3 21.5 459 n/a 4_occ: 0.1176 0.1358 0.006 0.949 9.3 104.3 21.5 459 n/a 5_bss: 0.1173 0.1360 0.006 0.949 9.3 104.3 21.5 459 n/a 5_settarget: 0.1173 0.1360 0.006 0.949 9.3 104.3 21.5 459 n/a 5_updatecdl: 0.1173 0.1360 0.006 0.950 9.3 104.3 21.5 459 n/a 5_setrh: 0.1174 0.1360 0.006 0.950 9.3 104.3 21.5 459 n/a 5_nqh: 0.1174 0.1360 0.006 0.950 9.3 104.3 21.5 459 n/a 5_sol: 0.1173 0.1341 0.006 0.950 9.3 104.3 21.4 461 n/a 5_weight: 0.1173 0.1341 0.006 0.950 9.3 104.3 21.4 461 n/a 5_xyzrec: 0.1204 0.1362 0.007 1.073 9.3 104.3 21.4 461 n/a 5_adp: 0.1206 0.1364 0.007 1.073 9.3 100.2 21.3 461 n/a 5_regHadp: 0.1206 0.1364 0.007 1.073 9.3 100.2 21.3 461 n/a 5_occ: 0.1203 0.1363 0.007 1.073 9.3 100.2 21.3 461 n/a end: 0.1204 0.1364 0.007 1.073 9.3 100.1 21.2 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9291273_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9291273_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.3900 Refinement macro-cycles (run) : 3408.9600 Write final files (write_after_run_outputs) : 74.9100 Total : 3488.2600 Total CPU time: 58.74 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:45 PST -0800 (1735452585.43 s) Start R-work = 0.1638, R-free = 0.1779 Final R-work = 0.1204, R-free = 0.1364 =============================================================================== Job complete usr+sys time: 3638.63 seconds wall clock time: 65 minutes 11.82 seconds (3911.82 seconds total)